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 * [[FreeSurferAnalysisPipelineOverview|Overview:]] General description of the functionality in !FreeSurfer
 * Recommended acquisition protocols:
 * '''[[FreeSurferAnalysisPipelineOverview|Overview:]]''' General description of the functionality in !FreeSurfer
 * '''Recommended acquisition protocols:'''
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 * Longitudinal studies:
  * [[LongitudinalProcessing|The longitudinal !FreeSurfer stream]]
 * '''Longitudinal studies:'''
  * [[LongitudinalProcessing|The longitudinal FreeSurfer stream]]
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 * Troubleshooting:  * '''Troubleshooting:'''
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 * Advanced:  * '''Advanced:'''
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 * [[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]] FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.  * '''[[FsFast|FreeSurfer Functional Analysis Stream (FS-FAST):]]''' FS-FAST is a set of tools for performing functional MRI data analyses on the cortical surface.
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 * [[Tracula|TRActs Constrained by UnderLying Anatomy (TRACULA):]] TRACULA is a tool for automated probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data.  * '''[[Tracula|TRActs Constrained by UnderLying Anatomy (TRACULA):]]''' TRACULA is a tool for automated probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data.
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 * [[FreeSurferCommandsRegistration|Registration tools:]] !FreeSurfer offers a range of tools for both within-subject and across-subject registration.  * '''[[FreeSurferCommandsRegistration|Registration tools:]]''' !FreeSurfer offers a range of tools for both within-subject and across-subject registration.

FreeSurfer

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.

  • License: The license agreement that allows you to use FreeSurfer

  • Release notes: New features and changes in each version of FreeSurfer - current stable release is v5.3.0

  • Installation guide: How to download and install FreeSurfer on your computer

  • Documentation: Getting started, step-by-step tutorials, FAQ, Glossary

  • Citing FreeSurfer: Short description and citations for core FreeSurfer methods

  • Publications: A Zotero library of articles on the methods in FreeSurfer and the studies that use FreeSurfer

  • User support: How to get help with problems that you encounter when using FreeSurfer

  • Hands-on training: Information on the FreeSurfer courses that we organize in Boston and around the world

  • User contributions: Scripts and techniques from users of FreeSurfer

  • Other software: Third-party software packages that are interoperable or related to FreeSurfer

  • Acknowledgements: The funding agencies and collaborators that have contributed to the research behind FreeSurfer

  • Social media: Find us on Facebook as FreeSurferMRI Find FreeSurferMRI on Facebook, follow us on Twitter Follow FreeSurferMRI on Twitter or join our LinkedIn group !LinkedIn FreeSurfer Group.

Our tools

Structural MRI

FreeSurfer provides a full processing stream for structural MRI data, including:

  • Skull stripping, B1 bias field correction, and gray-white matter segmentation
  • Reconstruction of cortical surface models (gray-white boundary surface and pial surface)
  • Labeling of regions on the cortical surface, as well as subcortical brain structures
  • Nonlinear registration of the cortical surface of an individual with a stereotaxic atlas
  • Statistical analysis of group morphometry differences

For more information, see:

Functional MRI

Diffusion MRI

  • TRActs Constrained by UnderLying Anatomy (TRACULA): TRACULA is a tool for automated probabilistic tractography with anatomical priors. It reconstructs a set of major white-matter pathways by incorporating prior information on the structural segmentation labels that each pathway goes through or next to, at every point long the pathway's trajectory. It includes a specialized stream for processing longitudinal diffusion MRI data.

Multimodal

  • Registration tools: FreeSurfer offers a range of tools for both within-subject and across-subject registration.

FreeSurferWiki (last edited 2019-07-18 11:36:01 by 172)